General information for g3962.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein TIS11.
Parent gene
- The parent gene g3962 is located on chr_3: 29301097..29301897 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g3962 | g3962.t4 | TSS | g3962.t4 | 29290127 | 29290127 |
| chr_3 | g3962 | g3962.t4 | isoform | g3962.t4 | 29290391 | 29300895 |
| chr_3 | g3962 | g3962.t4 | exon | g3962.t4.exon1 | 29290391 | 29290457 |
| chr_3 | g3962 | g3962.t4 | exon | g3962.t4.exon2 | 29300276 | 29300628 |
| chr_3 | g3962 | g3962.t4 | cds | g3962.t4.CDS1 | 29300351 | 29300628 |
| chr_3 | g3962 | g3962.t4 | exon | g3962.t4.exon3 | 29300724 | 29300895 |
| chr_3 | g3962 | g3962.t4 | cds | g3962.t4.CDS2 | 29300724 | 29300895 |
| chr_3 | g3962 | g3962.t4 | TTS | g3962.t4 | 29301755 | 29301755 |
Sequences
>g3962.t4 Gene=g3962 Length=592
ATGTCTACTGCAATTTTACATGCTGGAACGTTTATTCACGATTTTAACGATCTAATAATA
AAGGTTAAATCAAAATACAAGTTCAAAGGCAATAGGCAATCAGAGCTATAAGGAGAAATT
TCAGCGAAAAGAGGATAACAATATGCATTTTTTGAAGCAACGAAATGACGCTTATATGAC
AAATTTGTTTGCAAGTCAACAAAAAAGAGCATTGCAAGATGTAATTGGGCAACAGCAGCA
ACAACAACATGCTGCATTAGCAAGAACAGTATCAACACCGATAACAGATACAAATCAATC
GGTCGTAAACAATCTTTTTACATCTCTCAATGATATTTTGAATGGAACAACTGCAACAAA
TGGACATCGTAAATTGGAACGTACACAGTCTGAGCCGTTACCACAAACTAATACATCACG
CTACAAAACGGAACTGTGTCGTCCTTTTGAGGAAGCAGGCGAATGCAAATATGGTGATAA
ATGTCAATTTGCTCATGGTTTTCATGAATTGCGTAACTTGCAACGTCATCCAAAATATAA
GACGGAATTGTGTCGCACTTTCCATAGCGTTGGCTTCTGCCCATATGGAGCA
>g3962.t4 Gene=g3962 Length=150
MHFLKQRNDAYMTNLFASQQKRALQDVIGQQQQQQHAALARTVSTPITDTNQSVVNNLFT
SLNDILNGTTATNGHRKLERTQSEPLPQTNTSRYKTELCRPFEEAGECKYGDKCQFAHGF
HELRNLQRHPKYKTELCRTFHSVGFCPYGA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3962.t4 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 87 | 125 | 0.000000 |
| 10 | g3962.t4 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 126 | 150 | 0.000000 |
| 3 | g3962.t4 | PANTHER | PTHR12547 | CCCH ZINC FINGER/TIS11-RELATED | 73 | 149 | 0.000000 |
| 4 | g3962.t4 | PANTHER | PTHR12547:SF53 | MRNA DECAY ACTIVATOR PROTEIN ZFP36L1 | 73 | 149 | 0.000000 |
| 2 | g3962.t4 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 94 | 120 | 0.000000 |
| 1 | g3962.t4 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 132 | 150 | 0.000120 |
| 11 | g3962.t4 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 93 | 121 | 16.643000 |
| 12 | g3962.t4 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 131 | 150 | 10.587000 |
| 8 | g3962.t4 | SMART | SM00356 | c3hfinal6 | 93 | 120 | 0.000000 |
| 7 | g3962.t4 | SMART | SM00356 | c3hfinal6 | 131 | 150 | 3.800000 |
| 5 | g3962.t4 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 90 | 125 | 0.000000 |
| 6 | g3962.t4 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 128 | 149 | 0.000072 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046872 | metal ion binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
